You need an ohm meter. A DMM would be my first choice, but anything that reads ohms will work. You are essentially reading each coil for resistance. I don't know much about the 2.3, but from a little research turns up that each coil should be about 13k-15k ohms. The terminals on the side for the plug in should be close to zero. It looks like cylinder 1&4 are one coil, and 2&3 are another. Simply put a probe in each and read the resistance, then warm the engine, and do it again.
You kind of have scattered posts throughout the forum, but from what I gather, your truck ran ok, then you parked it. Now it runs rough, correct? To me this screams fuel problem.
I can't find anywhere on this thread where you posted fuel pressure, assuming you tested it.
The best thing you could probably do right now is drive it as much as you dare, and try to get a good KOER and KOEO test.
As for the exhaust, manifold to 2" to 2.25" catback seems standard. Both my 4.0's have that. I think you have completely ruled out an exhaust problem.
No matter what, your engine is running extremely rich. It might not be a bad idea to pop out your fuel injectors and clean them good. I have no clue how hard it is on the 2.3, but is trivial on the 4.0. I have never heard of an an ignition problem causing a rich condition. Bad O2 sensors are also a very real possibility, but almost impossible to tell without an engine code.